@ncukondo/reference-manager 0.29.3 → 0.29.6

package/dist/chunks/{fix-interaction-DY3_z_EL.js.map → fix-interaction-B6FGIOz8.js.map}

@@ -1 +1 @@
-{"version":3,"file":"fix-interaction-DY3_z_EL.js","sources":["../../src/features/check/fix-actions.ts","../../src/features/check/fix-interaction.ts"],"sourcesContent":["import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport type { CheckFinding } from \"./types.js\";\n\nexport type FixActionType =\n  | \"add_retracted_tag\"\n  | \"add_retraction_note\"\n  | \"remove_from_library\"\n  | \"update_from_published\"\n  | \"add_version_tag\"\n  | \"add_concern_tag\"\n  | \"add_concern_note\"\n  | \"update_all_fields\"\n  | \"update_selected_fields\"\n  | \"skip\";\n\nexport interface FixAction {\n  type: FixActionType;\n  label: string;\n}\n\nexport interface FixActionResult {\n  applied: boolean;\n  message: string;\n  removed?: boolean;\n}\n\nexport function getFixActionsForFinding(finding: CheckFinding): FixAction[] {\n  switch (finding.type) {\n    case \"retracted\":\n      return [\n        { type: \"add_retracted_tag\", label: 'Add tag \"retracted\"' },\n        { type: \"add_retraction_note\", label: \"Add note with retraction details\" },\n        { type: \"remove_from_library\", label: \"Remove from library\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"version_changed\":\n      return [\n        { type: \"update_from_published\", label: \"Update metadata from published version\" },\n        { type: \"add_version_tag\", label: 'Add tag \"has-published-version\"' },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"concern\":\n      return [\n        { type: \"add_concern_tag\", label: 'Add tag \"expression-of-concern\"' },\n        { type: \"add_concern_note\", label: \"Add note with concern details\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"metadata_mismatch\":\n    case \"metadata_outdated\":\n      return [\n        { type: \"update_all_fields\", label: \"Update all changed fields from remote\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    default:\n      return [];\n  }\n}\n\nfunction addTag(item: CslItem, tag: string): string[] {\n  const existing = (item.custom?.tags as string[] | undefined) ?? [];\n  if (existing.includes(tag)) {\n    return existing;\n  }\n  return [...existing, tag];\n}\n\nfunction buildNoteText(prefix: string, finding: CheckFinding): string {\n  const parts = [prefix];\n  if (finding.details?.retractionDate) {\n    parts.push(`Date: ${finding.details.retractionDate}`);\n  }\n  if (finding.details?.retractionDoi) {\n    parts.push(`DOI: ${finding.details.retractionDoi}`);\n  }\n  return parts.join(\". \");\n}\n\nfunction appendNote(existingNote: string | undefined, newNote: string): string {\n  if (existingNote) {\n    return `${existingNote}\\n\\n${newNote}`;\n  }\n  return newNote;\n}\n\nasync function applyTagAction(\n  library: ILibrary,\n  item: CslItem,\n  tag: string\n): Promise<FixActionResult> {\n  const tags = addTag(item, tag);\n  await library.update(item.id, { custom: { ...item.custom, tags } } as Partial<CslItem>, {\n    idType: \"id\",\n  });\n  await library.save();\n  return { applied: true, message: `Added tag \"${tag}\"` };\n}\n\nasync function applyNoteAction(\n  library: ILibrary,\n  item: CslItem,\n  prefix: string,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const noteText = buildNoteText(prefix, finding);\n  const note = appendNote(item.note, noteText);\n  await library.update(item.id, { note } as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Added note: ${noteText}` };\n}\n\nasync function applyUpdateFromPublished(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const newDoi = finding.details?.newDoi;\n  if (!newDoi) {\n    return { applied: false, message: \"No published DOI available in finding details\" };\n  }\n  const { fetchDoi } = await import(\"../import/fetcher.js\");\n  const fetchResult = await fetchDoi(newDoi);\n  if (!fetchResult.success) {\n    return {\n      applied: false,\n      message: `Failed to fetch metadata for ${newDoi}: ${fetchResult.error}`,\n    };\n  }\n  const { id: _id, custom: _custom, ...metadata } = fetchResult.item;\n  await library.update(item.id, metadata as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Updated metadata from ${newDoi}` };\n}\n\nasync function applyUpdateAllFields(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  let fetchedItem: CslItem;\n\n  if (item.DOI) {\n    const { fetchDoi } = await import(\"../import/fetcher.js\");\n    const fetchResult = await fetchDoi(item.DOI);\n    if (!fetchResult.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for DOI ${item.DOI}: ${fetchResult.error}`,\n      };\n    }\n    fetchedItem = fetchResult.item;\n  } else if (item.PMID) {\n    const { fetchPmids } = await import(\"../import/fetcher.js\");\n    const results = await fetchPmids([item.PMID], {});\n    const result = results[0];\n    if (!result || !result.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for PMID ${item.PMID}: ${result?.error ?? \"unknown error\"}`,\n      };\n    }\n    fetchedItem = result.item;\n  } else {\n    return { applied: false, message: \"No DOI or PMID available for metadata update\" };\n  }\n\n  const updatedFields = finding.details?.updatedFields ?? 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API.\n    case \"update_selected_fields\":\n      return { applied: false, message: \"Field selection not available in CLI mode\" };\n\n    case \"skip\":\n      return { applied: true, message: \"Skipped\" };\n\n    default:\n      return { applied: false, message: `Unknown action: ${actionType}` };\n  }\n}\n","import { render } from \"ink\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { restoreStdinAfterInk } from \"../interactive/alternate-screen.js\";\nimport { Select } from \"../interactive/components/index.js\";\nimport type { SelectOption } from \"../interactive/components/index.js\";\nimport { type FixActionType, applyFixAction, getFixActionsForFinding } from \"./fix-actions.js\";\nimport type { CheckFinding, CheckResult } from \"./types.js\";\n\nexport interface FixInteractionResult {\n  totalFindings: number;\n  applied: number;\n  skipped: number;\n  removed: string[];\n}\n\nfunction selectFixAction(\n  message: string,\n  options: SelectOption<FixActionType>[]\n): Promise<FixActionType | null> {\n  return new Promise<FixActionType | null>((resolve) => {\n    let selected: FixActionType | null = null;\n\n    const { waitUntilExit } = render(\n      createElement(Select<FixActionType>, {\n        options,\n        message,\n        onSelect: (value: FixActionType) => {\n          selected = value;\n        },\n        onCancel: () => {\n          selected = null;\n        },\n      })\n    );\n\n    waitUntilExit()\n      .then(() => {\n        restoreStdinAfterInk();\n        resolve(selected);\n      })\n      .catch(() => {\n        restoreStdinAfterInk();\n        resolve(null);\n      });\n  });\n}\n\nfunction getStatusLabel(type: string): string {\n  switch (type) {\n    case \"retracted\":\n      return \"RETRACTED\";\n    case \"concern\":\n      return \"CONCERN\";\n    case \"version_changed\":\n      return 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selectedAction);\n\n  if (!actionResult.applied) {\n    process.stderr.write(`  Error: ${actionResult.message}\\n`);\n    return;\n  }\n\n  process.stderr.write(`  ${actionResult.message}\\n`);\n  if (selectedAction === \"skip\") {\n    result.skipped++;\n  } else {\n    result.applied++;\n    if (actionResult.removed) {\n      result.removed.push(resultId);\n    }\n  }\n}\n\nexport async function runFixInteraction(\n  results: CheckResult[],\n  library: ILibrary,\n  findItem: (id: string) => CslItem | undefined\n): Promise<FixInteractionResult> {\n  const interactionResult: FixInteractionResult = {\n    totalFindings: 0,\n    applied: 0,\n    skipped: 0,\n    removed: [],\n  };\n\n  const warningResults = results.filter((r) => r.status === \"warning\");\n\n  for (const checkResult of warningResults) {\n    const item = findItem(checkResult.id);\n    if (!item) continue;\n\n    for (const finding of checkResult.findings) {\n      await processFinding(interactionResult, library, item, 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API.\n    case \"update_selected_fields\":\n      return { applied: false, message: \"Field selection not available in CLI mode\" };\n\n    case \"skip\":\n      return { applied: true, message: \"Skipped\" };\n\n    default:\n      return { applied: false, message: `Unknown action: ${actionType}` };\n  }\n}\n","import { render } from \"ink\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { restoreStdinAfterInk } from \"../interactive/alternate-screen.js\";\nimport { Select } from \"../interactive/components/index.js\";\nimport type { SelectOption } from \"../interactive/components/index.js\";\nimport { type FixActionType, applyFixAction, getFixActionsForFinding } from \"./fix-actions.js\";\nimport type { CheckFinding, CheckResult } from \"./types.js\";\n\nexport interface FixInteractionResult {\n  totalFindings: number;\n  applied: number;\n  skipped: 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selectedAction);\n\n  if (!actionResult.applied) {\n    process.stderr.write(`  Error: ${actionResult.message}\\n`);\n    return;\n  }\n\n  process.stderr.write(`  ${actionResult.message}\\n`);\n  if (selectedAction === \"skip\") {\n    result.skipped++;\n  } else {\n    result.applied++;\n    if (actionResult.removed) {\n      result.removed.push(resultId);\n    }\n  }\n}\n\nexport async function runFixInteraction(\n  results: CheckResult[],\n  library: ILibrary,\n  findItem: (id: string) => CslItem | undefined\n): Promise<FixInteractionResult> {\n  const interactionResult: FixInteractionResult = {\n    totalFindings: 0,\n    applied: 0,\n    skipped: 0,\n    removed: [],\n  };\n\n  const warningResults = results.filter((r) => r.status === \"warning\");\n\n  for (const checkResult of warningResults) {\n    const item = findItem(checkResult.id);\n    if (!item) continue;\n\n    for (const finding of checkResult.findings) {\n      await processFinding(interactionResult, library, item, 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package/dist/chunks/{index-BIFGa9-R.js → index-CGV9-f_j.js}

@@ -1,5 +1,5 @@
 import { a } from "./index-6Aild0Uk.js";
-import { d, g, l, o, s } from "./index-CVWiZowt.js";
+import { d, g, l, o, s } from "./index-Czz9ZhIH.js";
 export {
   a as addAttachment,
   d as detachAttachment,
@@ -8,4 +8,4 @@ export {
   o as openAttachment,
   s as syncAttachments
 };
-//# sourceMappingURL=index-BIFGa9-R.js.map
+//# sourceMappingURL=index-CGV9-f_j.js.map

package/dist/chunks/index-CGV9-f_j.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index-CGV9-f_j.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;"}

package/dist/chunks/{index-CVWiZowt.js → index-Czz9ZhIH.js}

@@ -19,7 +19,7 @@ import "@citation-js/plugin-csl";
 import { ZodOptional as ZodOptional$2, z } from "zod";
 import { serve } from "@hono/node-server";
 const name = "@ncukondo/reference-manager";
-const version$1 = "0.29.3";
+const version$1 = "0.29.6";
 const description$1 = "A local reference management tool using CSL-JSON as the single source of truth";
 const packageJson = {
   name,
@@ -929,27 +929,27 @@ class OperationsLibrary {
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-BIFGa9-R.js");
+    const { addAttachment: addAttachment2 } = await import("./index-CGV9-f_j.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-BIFGa9-R.js");
+    const { listAttachments: listAttachments2 } = await import("./index-CGV9-f_j.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-BIFGa9-R.js");
+    const { getAttachment: getAttachment2 } = await import("./index-CGV9-f_j.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-BIFGa9-R.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-CGV9-f_j.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-BIFGa9-R.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-CGV9-f_j.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-BIFGa9-R.js");
+    const { openAttachment: openAttachment2 } = await import("./index-CGV9-f_j.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1256,6 +1256,15 @@ class ServerClient {
     return await response.json();
   }
 }
+function getCliSpawnArgs(cliArgs) {
+  const scriptPath = process.argv[1];
+  const isCompiledBinary = scriptPath !== void 0 && (scriptPath === process.execPath || scriptPath.startsWith("/$bunfs/"));
+  if (isCompiledBinary) {
+    return { command: process.execPath, args: cliArgs };
+  }
+  const script = scriptPath || process.execPath;
+  return { command: process.execPath, args: [script, ...cliArgs] };
+}
 async function getServerConnection(libraryPath, config2) {
   const portfilePath = getPortfilePath();
   const portfileData = await readPortfile(portfilePath);
@@ -1280,8 +1289,8 @@ async function getServerConnection(libraryPath, config2) {
   };
 }
 async function startServerDaemon$1(libraryPath, _config) {
-  const binaryPath = process.argv[1] || process.execPath;
-  const child = spawn(process.execPath, [binaryPath, "server", "start", "--library", libraryPath], {
+  const { command, args } = getCliSpawnArgs(["server", "start", "--library", libraryPath]);
+  const child = spawn(command, args, {
     detached: true,
     stdio: "ignore"
   });
@@ -1805,7 +1814,7 @@ function getAttachExitCode(result) {
 }
 async function executeInteractiveSelect$2(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-C2HqrmMq.js");
+  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2470,7 +2479,7 @@ async function handleCheckAction(identifiers, options, globalOpts) {
     const jsonOptions = buildJsonOptionsFromRefs(options, outputFormat, result, allRefs);
     outputCheckResult(result, outputFormat, jsonOptions);
     if (options.fix && result.summary.warnings > 0 && allRefs) {
-      const { runFixInteraction } = await import("./fix-interaction-DY3_z_EL.js");
+      const { runFixInteraction } = await import("./fix-interaction-B6FGIOz8.js");
       const findItem = (id2) => allRefs.find((item) => item.id === id2);
       const fixResult = await runFixInteraction(result.results, context.library, findItem);
       const removedSuffix = fixResult.removed.length > 0 ? `, ${fixResult.removed.length} removed` : "";
@@ -2538,7 +2547,7 @@ function outputCheckError(error, format2) {
 }
 async function selectReferencesInteractively(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-C2HqrmMq.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-Hc3wU8jL.js");
   const allReferences = await context.library.getAll();
   if (allReferences.length === 0) {
     process.stderr.write("No references in library.\n");
@@ -2606,8 +2615,8 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-BS4fr4Ed.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-BAWNPFax.js");
+  const { runCiteFlow } = await import("./index-KAr1YWtM.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-CcRnu0nC.js");
   const { search } = await import("./file-watcher-CWHg1yol.js").then((n) => n.B);
   const { tokenize } = await import("./file-watcher-CWHg1yol.js").then((n) => n.A);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
@@ -7208,7 +7217,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-C2HqrmMq.js");
+  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10770,7 +10779,7 @@ function getFulltextExitCode(result) {
 }
 async function executeInteractiveSelect$1(context, config2, multiSelect = false) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-C2HqrmMq.js");
+  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect }, config2.cli.tui)
@@ -32280,7 +32289,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-C2HqrmMq.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-Hc3wU8jL.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32505,7 +32514,7 @@ async function executeInteractiveSearch(options, context, config2) {
   validateInteractiveOptions(options);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runSearchFlow } = await import("./index-BS4fr4Ed.js");
+  const { runSearchFlow } = await import("./index-KAr1YWtM.js");
   const { search } = await import("./file-watcher-CWHg1yol.js").then((n) => n.B);
   const { tokenize } = await import("./file-watcher-CWHg1yol.js").then((n) => n.A);
   checkTTY();
@@ -32524,7 +32533,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-DYfuYmAl.js");
+    const { isSideEffectAction } = await import("./action-menu-C4nIA-Sl.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32646,12 +32655,12 @@ async function serverStart(options) {
   await startServerForeground(options);
 }
 async function startServerDaemon(options) {
-  const binaryPath = process.argv[1] || process.execPath;
-  const args = [binaryPath, "server", "start", "--library", options.library];
+  const cliArgs = ["server", "start", "--library", options.library];
   if (options.port !== void 0) {
-    args.push("--port", String(options.port));
+    cliArgs.push("--port", String(options.port));
   }
-  const child = spawn(process.execPath, args, {
+  const { command, args } = getCliSpawnArgs(cliArgs);
+  const child = spawn(command, args, {
     detached: true,
     stdio: "ignore"
   });
@@ -32935,7 +32944,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-C2HqrmMq.js");
+  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33230,7 +33239,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-C2HqrmMq.js");
+  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -34079,4 +34088,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-CVWiZowt.js.map
+//# sourceMappingURL=index-Czz9ZhIH.js.map